PDBsum entry 1bwf

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Transferase PDB id
Protein chains
494 a.a. *
ATF ×2
GOL ×2
_MG ×2
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Escherichia coli glycerol kinase mutant with bound atp analo substantial domain motion
Structure: Glycerol kinase. Chain: y, o. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Organ: seed. Tissue: platelet. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: cloned gene
Biol. unit: Homo-Dimer (from PDB file)
3.00Å     R-factor:   0.168    
Authors: C.E.Bystrom,D.W.Pettigrew,B.P.Branchaud,S.J.Remington
Key ref:
C.E.Bystrom et al. (1999). Crystal structures of Escherichia coli glycerol kinase variant S58-->W in complex with nonhydrolyzable ATP analogues reveal a putative active conformation of the enzyme as a result of domain motion. Biochemistry, 38, 3508-3518. PubMed id: 10090737 DOI: 10.1021/bi982460z
23-Sep-98     Release date:   18-May-99    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P0A6F3  (GLPK_ECOLI) -  Glycerol kinase
502 a.a.
494 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Glycerol kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + glycerol = ADP + sn-glycerol 3-phosphate
Bound ligand (Het Group name = GOL)
corresponds exactly
Bound ligand (Het Group name = ATF)
matches with 76.47% similarity
+ sn-glycerol 3-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytosol   1 term 
  Biological process     metabolic process   7 terms 
  Biochemical function     catalytic activity     9 terms  


DOI no: 10.1021/bi982460z Biochemistry 38:3508-3518 (1999)
PubMed id: 10090737  
Crystal structures of Escherichia coli glycerol kinase variant S58-->W in complex with nonhydrolyzable ATP analogues reveal a putative active conformation of the enzyme as a result of domain motion.
C.E.Bystrom, D.W.Pettigrew, B.P.Branchaud, P.O'Brien, S.J.Remington.
Escherichia coli glycerol kinase (GK) displays "half-of-the-sites" reactivity toward ATP and allosteric regulation by fructose 1, 6-bisphosphate (FBP), which has been shown to promote dimer-tetramer assembly and to inhibit only tetramers. To probe the role of tetramer assembly, a mutation (Ser58-->Trp) was designed to sterically block formation of the dimer-dimer interface near the FBP binding site [Ormo, M., Bystrom, C., and Remington, S. J. (1998) Biochemistry 37, 16565-16572]. The substitution did not substantially change the Michaelis constants or alter allosteric regulation of GK by a second effector, the phosphocarrier protein IIAGlc; however, it eliminated FBP inhibition. Crystal structures of GK in complex with different nontransferable ATP analogues and glycerol revealed an asymmetric dimer with one subunit adopting an open conformation and the other adopting the closed conformation found in previously determined structures. The conformational difference is produced by a approximately 6.0 degrees rigid-body rotation of the N-terminal domain with respect to the C-terminal domain, similar to that observed for hexokinase and actin, members of the same ATPase superfamily. Two of the ATP analogues bound in nonproductive conformations in both subunits. However, beta, gamma-difluoromethyleneadenosine 5'-triphosphate (AMP-PCF2P), a potent inhibitor of GK, bound nonproductively in the closed subunit and in a putative productive conformation in the open subunit, with the gamma-phosphate placed for in-line transfer to glycerol. This asymmetry is consistent with "half-of-the-sites" reactivity and suggests that the inhibition of GK by FBP is due to restriction of domain motion.

Literature references that cite this PDB file's key reference Google scholar

  PubMed id Reference
19040641 C.Schnick, S.D.Polley, Q.L.Fivelman, L.C.Ranford-Cartwright, S.R.Wilkinson, J.A.Brannigan, A.J.Wilkinson, and D.A.Baker (2009).
Structure and non-essential function of glycerol kinase in Plasmodium falciparum blood stages.
  Mol Microbiol, 71, 533-545.
PDB codes: 2w40 2w41
19056335 D.W.Pettigrew (2009).
Amino acid substitutions in the sugar kinase/hsp70/actin superfamily conserved ATPase core of E. coli glycerol kinase modulate allosteric ligand affinity but do not alter allosteric coupling.
  Arch Biochem Biophys, 481, 151-156.  
19819219 D.W.Pettigrew (2009).
Oligomeric interactions provide alternatives to direct steric modes of control of sugar kinase/actin/hsp70 superfamily functions by heterotropic allosteric effectors: inhibition of E. coli glycerol kinase.
  Arch Biochem Biophys, 492, 29-39.  
18422647 Y.Koga, R.Katsumi, D.J.You, H.Matsumura, K.Takano, and S.Kanaya (2008).
Crystal structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon in a dimeric form.
  FEBS J, 275, 2632-2643.
PDB code: 2zf5
17999468 A.Gorrell, and J.G.Ferry (2007).
Investigation of the Methanosarcina thermophila acetate kinase mechanism by fluorescence quenching.
  Biochemistry, 46, 14170-14176.  
17123542 E.Di Luccio, B.Petschacher, J.Voegtli, H.T.Chou, H.Stahlberg, B.Nidetzky, and D.K.Wilson (2007).
Structural and kinetic studies of induced fit in xylulose kinase from Escherichia coli.
  J Mol Biol, 365, 783-798.
PDB codes: 2itm 2nlx
  17277457 R.Katsumi, Y.Koga, D.J.You, H.Matsumura, K.Takano, and S.Kanaya (2007).
Crystallization and preliminary X-ray diffraction study of glycerol kinase from the hyperthermophilic archaeon Thermococcus kodakaraensis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 126-129.  
15647264 A.Gorrell, S.H.Lawrence, and J.G.Ferry (2005).
Structural and kinetic analyses of arginine residues in the active site of the acetate kinase from Methanosarcina thermophila.
  J Biol Chem, 280, 10731-10742.
PDB codes: 1tuu 1tuy
15774882 C.Ingram-Smith, A.Gorrell, S.H.Lawrence, P.Iyer, K.Smith, and J.G.Ferry (2005).
Characterization of the acetate binding pocket in the Methanosarcina thermophila acetate kinase.
  J Bacteriol, 187, 2386-2394.  
12509431 D.L.Jakeman, A.J.Ivory, G.M.Blackburn, and M.P.Williamson (2003).
Orientation of 1,3-bisphosphoglycerate analogs bound to phosphoglycerate kinase.
  J Biol Chem, 278, 10957-10962.  
12829462 P.Grayson, E.Tajkhorshid, and K.Schulten (2003).
Mechanisms of selectivity in channels and enzymes studied with interactive molecular dynamics.
  Biophys J, 85, 36-48.  
12829458 T.Schlick (2003).
Engineering teams up with computer-simulation and visualization tools to probe biomolecular mechanisms.
  Biophys J, 85, 1-4.  
12161559 A.C.Pawlyk, and D.W.Pettigrew (2002).
Transplanting allosteric control of enzyme activity by protein-protein interactions: coupling a regulatory site to the conserved catalytic core.
  Proc Natl Acad Sci U S A, 99, 11115-11120.  
12162561 S.Sakasegawa, H.Takehara, I.Yoshioka, H.Misaki, H.Sakuraba, and T.Ohshima (2002).
Stabilization of flavobacterium meningosepticum glycerol kinase by introduction of a hydrogen bond.
  Biosci Biotechnol Biochem, 66, 1374-1377.  
11418773 H.S.Huang, T.Inoue, K.Ito, and T.Yoshimoto (2001).
Preliminary crystallographic study of Thermus aquaticus glycerol kinase.
  Acta Crystallogr D Biol Crystallogr, 57, 1030-1031.  
10734184 W.G.Krebs, and M.Gerstein (2000).
The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework.
  Nucleic Acids Res, 28, 1665-1675.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.